mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 05:41:59 +02:00
(v2.1.1.9141) new AMR selectors, eucast overwrite arg
This commit is contained in:
@ -113,7 +113,7 @@ TAXONOMY_VERSION <- list(
|
||||
name = "Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT)",
|
||||
accessed_date = as.Date("2024-07-16"),
|
||||
citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
|
||||
url = "https://www.cdc.gov/phin/php/phinvads"
|
||||
url = "https://www.cdc.gov/phin/php/phinvads/"
|
||||
),
|
||||
LOINC = list(
|
||||
name = "Logical Observation Identifiers Names and Codes (LOINC)",
|
||||
|
||||
@ -403,6 +403,14 @@ glycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
|
||||
amr_select_exec("glycopeptides", only_sir_columns = only_sir_columns, return_all = return_all)
|
||||
}
|
||||
|
||||
#' @rdname antimicrobial_class_selectors
|
||||
#' @export
|
||||
isoxazolylpenicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(return_all, allow_class = "logical", has_length = 1)
|
||||
amr_select_exec("isoxazolylpenicillins", only_sir_columns = only_sir_columns, return_all = return_all)
|
||||
}
|
||||
|
||||
#' @rdname antimicrobial_class_selectors
|
||||
#' @export
|
||||
lincosamides <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
|
||||
@ -428,6 +436,14 @@ macrolides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
|
||||
amr_select_exec("macrolides", only_sir_columns = only_sir_columns, return_all = return_all)
|
||||
}
|
||||
|
||||
#' @rdname antimicrobial_class_selectors
|
||||
#' @export
|
||||
monobactams <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(return_all, allow_class = "logical", has_length = 1)
|
||||
amr_select_exec("monobactams", only_sir_columns = only_sir_columns, return_all = return_all)
|
||||
}
|
||||
|
||||
#' @rdname antimicrobial_class_selectors
|
||||
#' @export
|
||||
nitrofurans <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
|
||||
|
||||
@ -481,10 +481,10 @@ antibiogram.default <- function(x,
|
||||
x$`.mo` <- x[, col_mo, drop = TRUE]
|
||||
if (is.null(mo_transform)) {
|
||||
# leave as is, no transformation
|
||||
} else if (is.na(mo_transform)) {
|
||||
x$`.mo` <- NA_character_
|
||||
} else if (is.function(mo_transform)) {
|
||||
x$`.mo` <- mo_transform(x$`.mo`)
|
||||
} else if (is.na(mo_transform)) {
|
||||
x$`.mo` <- NA_character_
|
||||
} else if (mo_transform == "gramstain") {
|
||||
x$`.mo` <- mo_gramstain(x$`.mo`, language = language)
|
||||
} else if (mo_transform == "shortname") {
|
||||
@ -602,8 +602,8 @@ antibiogram.default <- function(x,
|
||||
on.exit(close(progress))
|
||||
|
||||
out$coverage <- NA_real_
|
||||
out$lower <- NA_real_
|
||||
out$upper <- NA_real_
|
||||
out$lower_ci <- NA_real_
|
||||
out$upper_ci <- NA_real_
|
||||
out$gamma_posterior <- NA_real_
|
||||
out$beta_posterior_1 <- NA_real_
|
||||
out$beta_posterior_2 <- NA_real_
|
||||
@ -657,8 +657,8 @@ antibiogram.default <- function(x,
|
||||
coverage_ci <- unname(stats::quantile(coverage_simulations, probs = probs))
|
||||
|
||||
out$coverage[i] <- coverage_mean
|
||||
out$lower[i] <- coverage_ci[1]
|
||||
out$upper[i] <- coverage_ci[2]
|
||||
out$lower_ci[i] <- coverage_ci[1]
|
||||
out$upper_ci[i] <- coverage_ci[2]
|
||||
}
|
||||
# remove progress bar from console
|
||||
close(progress)
|
||||
@ -705,8 +705,8 @@ antibiogram.default <- function(x,
|
||||
if (wisca == TRUE) {
|
||||
long_numeric <- out %pm>%
|
||||
pm_summarise(coverage = coverage,
|
||||
lower_ci = lower,
|
||||
upper_ci = upper,
|
||||
lower_ci = lower_ci,
|
||||
upper_ci = upper_ci,
|
||||
n_tested = total,
|
||||
n_total = total_rows,
|
||||
n_susceptible = numerator,
|
||||
@ -758,12 +758,12 @@ antibiogram.default <- function(x,
|
||||
if (formatting_type == 10) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), "% (", numerator, "/", total, ")"))
|
||||
if (formatting_type == 11) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), " (N=", numerator, "/", total, ")"))
|
||||
if (formatting_type == 12) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), "% (N=", numerator, "/", total, ")"))
|
||||
if (formatting_type == 13) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), ")"))
|
||||
if (formatting_type == 14) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), "%)"))
|
||||
if (formatting_type == 15) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), ",", total, ")"))
|
||||
if (formatting_type == 16) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), "%,", total, ")"))
|
||||
if (formatting_type == 17) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), ",N=", total, ")"))
|
||||
if (formatting_type == 18) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), "%,N=", total, ")"))
|
||||
if (formatting_type == 13) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), ")"))
|
||||
if (formatting_type == 14) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), "%)"))
|
||||
if (formatting_type == 15) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), ",", total, ")"))
|
||||
if (formatting_type == 16) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), "%,", total, ")"))
|
||||
if (formatting_type == 17) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), ",N=", total, ")"))
|
||||
if (formatting_type == 18) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), "%,N=", total, ")"))
|
||||
|
||||
# transform names of antibiotics
|
||||
ab_naming_function <- function(x, t, l, s) {
|
||||
@ -1100,11 +1100,11 @@ plot.antibiogram <- function(x, ...) {
|
||||
)
|
||||
|
||||
if (isTRUE(attributes(x)$wisca)) {
|
||||
lower <- df_sub$lower * 100
|
||||
upper <- df_sub$upper * 100
|
||||
lower_ci <- df_sub$lower_ci * 100
|
||||
upper_ci <- df_sub$upper_ci * 100
|
||||
arrows(
|
||||
x0 = bp, y0 = lower, # Start of error bar (lower bound)
|
||||
x1 = bp, y1 = upper, # End of error bar (upper bound)
|
||||
x0 = bp, y0 = lower_ci, # Start of error bar (lower bound)
|
||||
x1 = bp, y1 = upper_ci, # End of error bar (upper bound)
|
||||
angle = 90, code = 3, length = 0.05, col = "black"
|
||||
)
|
||||
}
|
||||
@ -1151,7 +1151,7 @@ autoplot.antibiogram <- function(object, ...) {
|
||||
)
|
||||
if (isTRUE(attributes(object)$wisca)) {
|
||||
out <- out +
|
||||
ggplot2::geom_errorbar(mapping = ggplot2::aes(ymin = lower * 100, ymax = upper * 100),
|
||||
ggplot2::geom_errorbar(mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
|
||||
position = ggplot2::position_dodge2(preserve = "single"),
|
||||
width = 0.5)
|
||||
}
|
||||
|
||||
@ -56,7 +56,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' Apply EUCAST Rules
|
||||
#'
|
||||
#' @description
|
||||
#' Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
|
||||
#' Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
|
||||
#'
|
||||
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
|
||||
#' @param x a data set with antibiotic columns, such as `amox`, `AMX` and `AMC`
|
||||
@ -72,6 +72,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' @param administration route of administration, either `r vector_or(dosage$administration)`
|
||||
#' @param only_sir_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`)
|
||||
#' @param custom_rules custom rules to apply, created with [custom_eucast_rules()]
|
||||
#' @param overwrite a [logical] to indicate whether non-`NA` values must be overwritten (defaults to `TRUE`). With `FALSE`, only `NA` values are changed.
|
||||
#' @inheritParams first_isolate
|
||||
#' @details
|
||||
#' **Note:** This function does not translate MIC values to SIR values. Use [as.sir()] for that. \cr
|
||||
@ -172,6 +173,7 @@ eucast_rules <- function(x,
|
||||
ampc_cephalosporin_resistance = NA,
|
||||
only_sir_columns = FALSE,
|
||||
custom_rules = NULL,
|
||||
overwrite = TRUE,
|
||||
...) {
|
||||
meet_criteria(x, allow_class = "data.frame")
|
||||
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
|
||||
@ -184,6 +186,7 @@ eucast_rules <- function(x,
|
||||
meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "sir"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE)
|
||||
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
|
||||
meet_criteria(overwrite, allow_class = "logical", has_length = 1)
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
@ -254,18 +257,18 @@ eucast_rules <- function(x,
|
||||
} else {
|
||||
# opening
|
||||
if (n_added > 0 && n_changed == 0) {
|
||||
cat(font_green(" ("))
|
||||
cat(font_bold(font_green(" (")))
|
||||
} else if (n_added == 0 && n_changed > 0) {
|
||||
cat(font_blue(" ("))
|
||||
cat(font_bold(font_blue(" (")))
|
||||
} else {
|
||||
cat(font_grey(" ("))
|
||||
}
|
||||
# additions
|
||||
if (n_added > 0) {
|
||||
if (n_added == 1) {
|
||||
cat(font_green("1 value added"))
|
||||
cat(font_bold(font_green("1 value added")))
|
||||
} else {
|
||||
cat(font_green(formatnr(n_added), "values added"))
|
||||
cat(font_bold(font_green(formatnr(n_added), "values added")))
|
||||
}
|
||||
}
|
||||
# separator
|
||||
@ -275,16 +278,16 @@ eucast_rules <- function(x,
|
||||
# changes
|
||||
if (n_changed > 0) {
|
||||
if (n_changed == 1) {
|
||||
cat(font_blue("1 value changed"))
|
||||
cat(font_bold(font_blue("1 value changed")))
|
||||
} else {
|
||||
cat(font_blue(formatnr(n_changed), "values changed"))
|
||||
cat(font_bold(font_blue(formatnr(n_changed), "values changed")))
|
||||
}
|
||||
}
|
||||
# closing
|
||||
if (n_added > 0 && n_changed == 0) {
|
||||
cat(font_green(")\n"))
|
||||
cat(font_bold(font_green(")\n")))
|
||||
} else if (n_added == 0 && n_changed > 0) {
|
||||
cat(font_blue(")\n"))
|
||||
cat(font_bold(font_blue(")\n")))
|
||||
} else {
|
||||
cat(font_grey(")\n"))
|
||||
}
|
||||
@ -327,6 +330,10 @@ eucast_rules <- function(x,
|
||||
}
|
||||
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
|
||||
}
|
||||
if (!"FOX" %in% names(cols_ab) && "FOX1" %in% names(cols_ab)) {
|
||||
# cefoxitin column is missing, but cefoxitin screening is available
|
||||
cols_ab <- c(cols_ab, c(FOX = unname(cols_ab[names(cols_ab) == "FOX1"])))
|
||||
}
|
||||
|
||||
# data preparation ----
|
||||
if (isTRUE(info) && NROW(x) > 10000) {
|
||||
@ -359,10 +366,8 @@ eucast_rules <- function(x,
|
||||
# like PEN,FOX S
|
||||
x <- paste(paste0(ab_names, collapse = " and "), "are both")
|
||||
} else {
|
||||
# like PEN,FOX,GEN S (although dependency on > 2 ABx does not exist at the moment)
|
||||
# nolint start
|
||||
# x <- paste(paste0(ab_names, collapse = " and "), "are all")
|
||||
# nolint end
|
||||
# like PEN,FOX,GEN S
|
||||
x <- paste(paste0(ab_names, collapse = " and "), "are all")
|
||||
}
|
||||
return(paste0(x, " '", ab_results, "'"))
|
||||
} else {
|
||||
@ -373,7 +378,7 @@ eucast_rules <- function(x,
|
||||
ab_names[2], " is '", ab_results[2], "'"
|
||||
)
|
||||
} else {
|
||||
# like PEN,FOX,GEN S,R,R (although dependency on > 2 ABx does not exist at the moment)
|
||||
# like PEN,FOX,GEN S,R,R
|
||||
paste0(
|
||||
ab_names[1], " is '", ab_results[1], "' and ",
|
||||
ab_names[2], " is '", ab_results[2], "' and ",
|
||||
@ -452,7 +457,7 @@ eucast_rules <- function(x,
|
||||
n_added <- 0
|
||||
n_changed <- 0
|
||||
|
||||
# Other rules: enzyme inhibitors ------------------------------------------
|
||||
# >>> Apply Other rules: enzyme inhibitors <<< ------------------------------------------
|
||||
if (any(c("all", "other") %in% rules)) {
|
||||
if (isTRUE(info)) {
|
||||
cat("\n")
|
||||
@ -488,7 +493,7 @@ eucast_rules <- function(x,
|
||||
col_base <- unname(cols_ab[ab_enzyme$base_ab[i]])
|
||||
col_enzyme <- unname(cols_ab[ab_enzyme$enzyme_ab[i]])
|
||||
|
||||
# Set base to R where base + enzyme inhibitor is R ----
|
||||
## Set base to R where base + enzyme inhibitor is R ----
|
||||
rule_current <- paste0(
|
||||
ab_enzyme$base_name[i], " ('", font_bold(col_base), "') = R if ",
|
||||
tolower(ab_enzyme$enzyme_name[i]), " ('", font_bold(col_enzyme), "') = R"
|
||||
@ -512,7 +517,8 @@ eucast_rules <- function(x,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info,
|
||||
verbose = verbose
|
||||
verbose = verbose,
|
||||
overwrite = overwrite
|
||||
)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
@ -528,7 +534,7 @@ eucast_rules <- function(x,
|
||||
n_changed <- 0
|
||||
}
|
||||
|
||||
# Set base + enzyme inhibitor to S where base is S ----
|
||||
## Set base + enzyme inhibitor to S where base is S ----
|
||||
rule_current <- paste0(
|
||||
ab_enzyme$enzyme_name[i], " ('", font_bold(col_enzyme), "') = S if ",
|
||||
tolower(ab_enzyme$base_name[i]), " ('", font_bold(col_base), "') = S"
|
||||
@ -584,7 +590,7 @@ eucast_rules <- function(x,
|
||||
custom_rules <- NULL
|
||||
}
|
||||
|
||||
# Official EUCAST rules ---------------------------------------------------
|
||||
# >>> Apply Official EUCAST rules <<< ---------------------------------------------------
|
||||
eucast_notification_shown <- FALSE
|
||||
if (!is.null(list(...)$eucast_rules_df)) {
|
||||
# this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
|
||||
@ -594,7 +600,7 @@ eucast_rules <- function(x,
|
||||
eucast_rules_df <- EUCAST_RULES_DF
|
||||
}
|
||||
|
||||
# filter on user-set guideline versions ----
|
||||
## filter on user-set guideline versions ----
|
||||
if (any(c("all", "breakpoints") %in% rules)) {
|
||||
eucast_rules_df <- subset(
|
||||
eucast_rules_df,
|
||||
@ -609,7 +615,7 @@ eucast_rules <- function(x,
|
||||
(reference.rule_group %like% "expert" & reference.version == version_expertrules)
|
||||
)
|
||||
}
|
||||
# filter out AmpC de-repressed cephalosporin-resistant mutants ----
|
||||
## filter out AmpC de-repressed cephalosporin-resistant mutants ----
|
||||
# no need to filter on version number here - the rules contain these version number, so are inherently filtered
|
||||
# cefotaxime, ceftriaxone, ceftazidime
|
||||
if (is.null(ampc_cephalosporin_resistance) || isFALSE(ampc_cephalosporin_resistance)) {
|
||||
@ -624,7 +630,7 @@ eucast_rules <- function(x,
|
||||
eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
|
||||
}
|
||||
|
||||
# Go over all rules and apply them ----
|
||||
## Go over all rules and apply them ----
|
||||
for (i in seq_len(nrow(eucast_rules_df))) {
|
||||
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule", drop = TRUE]
|
||||
rule_current <- eucast_rules_df[i, "reference.rule", drop = TRUE]
|
||||
@ -664,19 +670,19 @@ eucast_rules <- function(x,
|
||||
}
|
||||
|
||||
if (isTRUE(info)) {
|
||||
# Print EUCAST intro ------------------------------------------------------
|
||||
## Print EUCAST intro ------------------------------------------------------
|
||||
if (rule_group_current %unlike% "other" && eucast_notification_shown == FALSE) {
|
||||
cat(
|
||||
paste0(
|
||||
"\n", font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n",
|
||||
word_wrap("Rules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)")), "\n",
|
||||
font_blue("https://eucast.org/"), "\n"
|
||||
font_blue(font_url("https://eucast.org/")), "\n"
|
||||
)
|
||||
)
|
||||
eucast_notification_shown <- TRUE
|
||||
}
|
||||
|
||||
# Print rule (group) ------------------------------------------------------
|
||||
## Print rule (group) ------------------------------------------------------
|
||||
if (rule_group_current != rule_group_previous) {
|
||||
# is new rule group, one of Breakpoints, Expert Rules and Other
|
||||
cat(font_bold(
|
||||
@ -703,7 +709,7 @@ eucast_rules <- function(x,
|
||||
)
|
||||
), "\n")
|
||||
}
|
||||
# Print rule -------------------------------------------------------------
|
||||
## Print rule -------------------------------------------------------------
|
||||
if (rule_current != rule_previous) {
|
||||
# is new rule within group, print its name
|
||||
cat(italicise_taxonomy(
|
||||
@ -717,7 +723,7 @@ eucast_rules <- function(x,
|
||||
}
|
||||
}
|
||||
|
||||
# Get rule from file ------------------------------------------------------
|
||||
## Get rule from file ------------------------------------------------------
|
||||
if_mo_property <- trimws(eucast_rules_df[i, "if_mo_property", drop = TRUE])
|
||||
like_is_one_of <- trimws(eucast_rules_df[i, "like.is.one_of", drop = TRUE])
|
||||
mo_value <- trimws(eucast_rules_df[i, "this_value", drop = TRUE])
|
||||
@ -824,7 +830,7 @@ eucast_rules <- function(x,
|
||||
|
||||
cols <- get_ab_from_namespace(target_antibiotics, cols_ab)
|
||||
|
||||
# Apply rule on data ------------------------------------------------------
|
||||
## Apply rule on data ------------------------------------------------------
|
||||
# this will return the unique number of changes
|
||||
run_changes <- edit_sir(
|
||||
x = x,
|
||||
@ -842,14 +848,15 @@ eucast_rules <- function(x,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info,
|
||||
verbose = verbose
|
||||
verbose = verbose,
|
||||
overwrite = overwrite
|
||||
)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
x <- run_changes$output
|
||||
warn_lacking_sir_class <- c(warn_lacking_sir_class, run_changes$sir_warn)
|
||||
# Print number of new changes ---------------------------------------------
|
||||
## Print number of new changes ---------------------------------------------
|
||||
if (isTRUE(info) && rule_next != rule_current) {
|
||||
# print only on last one of rules in this group
|
||||
txt_ok(n_added = n_added, n_changed = n_changed, warned = warned)
|
||||
@ -859,7 +866,7 @@ eucast_rules <- function(x,
|
||||
}
|
||||
} # end of going over all rules
|
||||
|
||||
# Apply custom rules ----
|
||||
# >>> Apply custom rules <<< ----
|
||||
if (!is.null(custom_rules)) {
|
||||
if (isTRUE(info)) {
|
||||
cat("\n")
|
||||
@ -910,14 +917,15 @@ eucast_rules <- function(x,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info,
|
||||
verbose = verbose
|
||||
verbose = verbose,
|
||||
overwrite = overwrite
|
||||
)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
x <- run_changes$output
|
||||
warn_lacking_sir_class <- c(warn_lacking_sir_class, run_changes$sir_warn)
|
||||
# Print number of new changes ---------------------------------------------
|
||||
## Print number of new changes ---------------------------------------------
|
||||
if (isTRUE(info) && rule_next != rule_current) {
|
||||
# print only on last one of rules in this group
|
||||
txt_ok(n_added = n_added, n_changed = n_changed, warned = warned)
|
||||
@ -940,6 +948,10 @@ eucast_rules <- function(x,
|
||||
pm_select(row, pm_everything()) %pm>%
|
||||
pm_filter(!is.na(new) | is.na(new) & !is.na(old)) %pm>%
|
||||
pm_arrange(row, rule_group, rule_name, col)
|
||||
if (isFALSE(overwrite)) {
|
||||
verbose_info <- verbose_info %pm>%
|
||||
pm_filter(!old %in% levels(NA_sir_))
|
||||
}
|
||||
rownames(verbose_info) <- NULL
|
||||
}
|
||||
|
||||
@ -1074,7 +1086,8 @@ edit_sir <- function(x,
|
||||
original_data,
|
||||
warned,
|
||||
info,
|
||||
verbose) {
|
||||
verbose,
|
||||
overwrite) {
|
||||
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
|
||||
|
||||
# for Verbose Mode, keep track of all changes and return them
|
||||
@ -1101,9 +1114,14 @@ edit_sir <- function(x,
|
||||
if (any(!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir), na.rm = TRUE)) {
|
||||
track_changes$sir_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir)]
|
||||
}
|
||||
non_SIR <- !(new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
|
||||
tryCatch(
|
||||
# insert into original table
|
||||
new_edits[rows, cols] <- to,
|
||||
if (isTRUE(overwrite)) {
|
||||
new_edits[rows, cols] <- to
|
||||
} else {
|
||||
new_edits[rows, cols][non_SIR] <- to
|
||||
},
|
||||
warning = function(w) {
|
||||
if (w$message %like% "invalid factor level") {
|
||||
xyz <- vapply(FUN.VALUE = logical(1), cols, function(col) {
|
||||
@ -1113,7 +1131,11 @@ edit_sir <- function(x,
|
||||
)
|
||||
TRUE
|
||||
})
|
||||
suppressWarnings(new_edits[rows, cols] <<- to)
|
||||
if (isTRUE(overwrite)) {
|
||||
suppressWarnings(new_edits[rows, cols] <<- to)
|
||||
} else {
|
||||
suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
|
||||
}
|
||||
warning_(
|
||||
"in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
|
||||
ifelse(length(cols) == 1, "", "s"),
|
||||
|
||||
@ -51,8 +51,8 @@
|
||||
#' @param include_untested_sir a [logical] to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_sir = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `sir` and consequently requires transforming columns with antibiotic results using [as.sir()] first.
|
||||
#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], otherwise arguments passed on to [key_antimicrobials()] (such as `universal`, `gram_negative`, `gram_positive`)
|
||||
#' @details
|
||||
#' The methodology implemented in these functions is based on the research overview by Hindler *et al.* (2007, \doi{10.1086/511864}) and the recommendations outlined in the [CLSI Guideline M39](https://clsi.org/standards/products/microbiology/documents/m39).
|
||||
|
||||
#' The methodology implemented in these functions is strictly based on the recommendations outlined in [CLSI Guideline M39](https://clsi.org/standards/products/microbiology/documents/m39) and the research overview by Hindler *et al.* (2007, \doi{10.1086/511864}).
|
||||
#'
|
||||
#' To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.
|
||||
#'
|
||||
#' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
|
||||
@ -126,7 +126,7 @@
|
||||
#' @seealso [key_antimicrobials()]
|
||||
#' @export
|
||||
#' @return A [logical] vector
|
||||
#' @source Methodology of this function is strictly based on:
|
||||
#' @source Methodology of these functions is strictly based on:
|
||||
#'
|
||||
#' - **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition**, 2022, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
|
||||
#'
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
Reference in New Issue
Block a user